[gmx-users] Printing energies at every step of energy minimization

[Justin Lemkul]

On 8/8/19 5:04 PM, Wahl, David M wrote:
> Hello,
>
>
> I am working on parameterizing a small molecule using GROMACS and am having issues during energy minimization.  I want the program to output the potential energy at every step, except it only prints at the initial step. The program shows that it takes another 7 steps, although it does not print any additional energies, as seen below:
>
>
> Steepest Descents:
>
>     Tolerance (Fmax)   =  1.00000e+01
>
>     Number of steps    =       500000
>
>
>             Step           Time
>
>                0        0.00000
>
>
>     Energies (kJ/mol)
>
>             Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>
>      1.13615e+00    7.60033e+00    9.76498e+00    1.07286e-02    2.59349e+01
>
>       Coulomb-14        LJ (SR)   Coulomb (SR)     Dih. Rest.      Potential
>
>     -1.42676e+03   -2.64334e+00    4.22198e+02    2.83276e-03   -9.62758e+02
>
>   Pressure (bar)
>
>      0.00000e+00
>
>
>             Step           Time
>
>                1        1.00000
>
>
>             Step           Time
>
>                2        2.00000
>
>
>             Step           Time
>
>                3        3.00000
>
>
>             Step           Time
>
>                4        4.00000
>
>
>             Step           Time
>
>                5        5.00000
>
>
>             Step           Time
>
>                6        6.00000
>
>
>             Step           Time
>
>
>                7        7.00000
>
>
>
> I have also tried changing nstlog, nstcalcenergy, and nstenergy all to 1 in the mdp file, although this yielded the same result as above.  Running mdrun verbose with the -v flag did not change anything either. I understand that they may not be printing because the energies are relatively close, but we still would like it to print all of the energies regardless of how small the differences.
>
>
>
> Any insight/recommendations would be greatly appreciated!

mdrun will not print energies during EM if the energy doesn't change or 
increases. If you want different behavior, you will have to change how 
the minimizer prints output in src/gromacs/mdrun/minimize.cpp.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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